Author: jgao
Date: 2010-02-18 19:33:30 -0800 (Thu, 18 Feb 2010)
New Revision: 19384
Modified:
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/IDMapperClientImplTunables.java
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/CyThesaurusDialog.java
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/IDMappingSourceConfigDialog.java
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/IDMappingSourceSelectionTree.java
Log:
CyThesaurus: disable AttributeMapping for BridgeRest (the service is too slow)
Modified:
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/IDMapperClientImplTunables.java
===================================================================
---
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/IDMapperClientImplTunables.java
2010-02-19 01:54:14 UTC (rev 19383)
+++
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/IDMapperClientImplTunables.java
2010-02-19 03:33:30 UTC (rev 19384)
@@ -216,6 +216,13 @@
Class.forName(getClassString());
mapper = BridgeDb.connect(getConnectionString());
preprocess(mapper);
+
+ // in case the current type is wrong, update it.
+ ClientType type = ClientType.getClientType(mapper);
+ if (type!=getClientType()) {
+ clientType.setValue(type.name());
+ props.saveProperties(clientType);
+ }
} catch (Exception e) {
e.printStackTrace();
return null;
Modified:
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/CyThesaurusDialog.java
===================================================================
---
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/CyThesaurusDialog.java
2010-02-19 01:54:14 UTC (rev 19383)
+++
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/CyThesaurusDialog.java
2010-02-19 03:33:30 UTC (rev 19384)
@@ -636,6 +636,10 @@
continue;
}
+ // TODO: remove next two lines after the problem of
AttributeMapper in BridgeRest is solved.
+ if (mapper instanceof
org.bridgedb.webservice.bridgerest.BridgeRest)
+ continue;
+
if (!(mapper instanceof AttributeMapper))
continue;
@@ -684,15 +688,20 @@
IDMapperStack stack = new IDMapperStack();
for (IDMapperClient client :
IDMapperClientManager.selectedClients()) {
IDMapper mapper = client.getIDMapper();
- if (mapper==null) {
+ if (mapper==null)
continue;
- }
- if (!(mapper instanceof IDMapperBiomart)) {
- // TODO: this is temperory solution
- // there should be a AttributeMapperCapacities or
something like that
- stack.addIDMapper(mapper);
- }
+ // TODO: IDMapperBiomart does not support mapping from
attribute
+ // this is temperory solution
+ // there should be a AttributeMapperCapacities or something
like that
+ if (mapper instanceof IDMapperBiomart)
+ continue;
+
+ // TODO: remove next line after the problem of AttributeMapper
in BridgeRest is solved.
+ if (mapper instanceof
org.bridgedb.webservice.bridgerest.BridgeRest)
+ continue;
+
+ stack.addIDMapper(mapper);
}
try {
srcAttrs = stack.getAttributeSet();
@@ -716,6 +725,10 @@
if (mapper==null || !(mapper instanceof AttributeMapper))
continue;
+ // TODO: remove next two lines after the problem of
AttributeMapper in BridgeRest is solved.
+ if (mapper instanceof
org.bridgedb.webservice.bridgerest.BridgeRest)
+ continue;
+
Set<String> attrs = null;
Set<DataSource> srcTypes = null;
try {
Modified:
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/IDMappingSourceConfigDialog.java
===================================================================
---
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/IDMappingSourceConfigDialog.java
2010-02-19 01:54:14 UTC (rev 19383)
+++
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/IDMappingSourceConfigDialog.java
2010-02-19 03:33:30 UTC (rev 19384)
@@ -266,7 +266,7 @@
IDMapperClientManager.reloadFromCytoscapeGlobalProperties();
- srcTree.reload();
+ srcTree.reset();
JOptionPane.showMessageDialog(this, "The default resources has been
loaded.");
}//GEN-LAST:event_loadDefaultButtonActionPerformed
@@ -379,6 +379,8 @@
// desc.append(capabilities.isFreeSearchSupported()?
"\tYes":"\tNo");
// desc.append("\n");
+ // TODO: remove next line after the problem of AttributeMapper in
BridgeRest is solved.
+ if (!(idMapper instanceof
org.bridgedb.webservice.bridgerest.BridgeRest))
if (idMapper instanceof AttributeMapper) {
desc.append(">>Supported Attributes\n");
Set<String> attrs =
((AttributeMapper)idMapper).getAttributeSet();
Modified:
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/IDMappingSourceSelectionTree.java
===================================================================
---
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/IDMappingSourceSelectionTree.java
2010-02-19 01:54:14 UTC (rev 19383)
+++
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/IDMappingSourceSelectionTree.java
2010-02-19 03:33:30 UTC (rev 19384)
@@ -115,13 +115,17 @@
selection_Model = checkTreeManager.getSelectionModel();
- reload();
+ initTree();
}
- public void reload() {
+ public void reset() {
+ initTree();
+ modified = true;
+ }
+
+ private void initTree() {
setupTree();
setupMouse();
- modified = true;
}
public boolean isModified() {
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